// get_arg.h
//

#if !defined(GETARG_H)
#define GETARG_H

#include <string>
#include <sstream>


#include <program_options_helper.h>

class t_program_args : public program_options_helper::t_std_program_args_with_errors
{
public:
	std::string		orphaned_clades;
	std::string  	taxon1;
	std::string  	taxon2;
	std::string  	taxon1_name;
	std::string  	taxon2_name;
	std::string		out_path_format;
	bool			no_breakdown_by_ortholog_type;

	// for initializing this struct
	friend
	bool process_command_line_options(int argc, char* argv[], t_program_args& args);
};
#endif
